It turned out that there was a crack in the middle of the sideframe on the rear truck of my Intermountain CN FP9A and that’s why it was sitting slightly askew. Of course removing the sideframe was a little tricky, but after taking a good long look at it and using some Google-fu, it finally came off with out much of a problem. I will say that for a friction fit part it was on there pretty damn good.
Since there are no parts diagrams for Intermountain locomotives beside the AC-12 and the SD40T I managed to find parts diagrams for Stewart F units here - http://bowser-trains.com/Stewart/Instructions/F%20Unit.pdf
Turns out that they are very similiar.
The only real difference is that there are two vertical pins for the Intermountain instead of the 3 horizontal pins for the Stewart and the crossbraces on the end of the Intermountain.
I removed the shell, gently spread the ends of the sideframes to pop out the crossbraces, and then used a flat blade screwdriver to ease off the frame from the truck. The copper wheel wiper is glued into the frame, but can be easily popped out without any problem. The leaf spring part of the frame is a separate piece and can be removed from it.
It was the centre part of the frame that had the crack where the leaf spring is attached. There’s a replacement sideframe on the way from Intermountain so I can do a proper fix now.